Alan-Philippe Blanchard, Ph.D.

Since the July, 2006 aquisition of APG, I have worked for Applied Biosystems where I am a Scientific Fellow working on
improving our next-generation DNA sequencing platform.
From September 2004 to July 2006 I worked for what was called
Agencourt Personal Genomics (APG) in Beverly, MA. APG had developed a very
high throughput DNA sequencing instrument based on a chemistry using DNA
ligase instead of the customary polymerase-based Sanger sequencing. Using
our ligase-based approach allows us to sequence homopolymer stretches that are
problematic with polymerase-based sequencing-by-synthesis schemes. Our
instrument sequences many millions of short DNA fragments in parallel
giving it a potential throughput orders of magnitude greater than existing
Sanger sequencers.
Part of my contribution was inventing a scheme
that produces partial sequence information from two (or more) bases at each
cycle. This allows for the detection of certain classes of error beyond
what is possible with traditional single-base encodings.
A degree in math does come in handy at times.
On May 30, 2006 it was announced that Applied Biosystems of Foster City, CA had agreed to buy APG for $120M. They have
announced plans to start placing instruments based on our chemistry at customer sites in 2007.

From March to November of 2003 I was VP of Research and Development at Manteia SA, based in Coinsins, Switzerland.
Manteia went bankrupt and the assets were sold to Lynx (Hayward, CA) and Solexa (near Cambridge, UK).
Lynx and Solexa subsequently merged to become the present-day Solexa which has announced a sequencing instrument using
the Manteia DNA amplification technology (clusters).
Solxa was subsequently bought by Illumina of San Diego, CA.
I never made a dime off the Manteia gig, but the experience was invaluable at APG, starting day 1.
If anyone from Manteia is reading this, please send me a note. I'd love to know where everyone went.

My previous project was developing an instrument to
make arrays of DNA molecules using ink-jet printer technology. I started
this project while I was finishing up my Ph.D. at Caltech. It took another 4
years,
while I was a post-doc at the University of Washington, to bring the technology
to the point where venture capitalists get interested.
Rosetta Inpharmatics was founded in 1997 on
the basis of this and related technologies.
The ink-jet technology was licensed and transfered to
Agilent, who now sell
custom in situ synthesized DNA arrays using machines based on my designs.

Machines I designed at Agilent's production facilities.

Merck bought Rosetta in 2001 for $600M and I left shortly thereafter.

Ed Southern did much of the pioneering work on
synthetic DNA arrays at Oxford, and was the first person to suggest using
ink-jet technology for their manufacture. Ed founded
Oxford Gene Technology to commercialise
some of his inventions. For a while, OGT was using array makers that I designed.
Two of these machines found their way to London when part of OGT was aquired by
Arrow Therapeutics